Given the following code contained in a qmake project file:
QWT_LIB_BINARY=/usr/lib/libqwt-qt4.so
TEMP1 = $$basename(QWT_LIB_BINARY)
TEMP2 = $$replace(TEMP1, .so, )
QWT_LIB_NAME = $$replace(TEMP2, lib, )
message(QWT library name = $$QWT_LIB_NAME)
Eliminates the path, the 'lib' prefix and the '.so' suffix of the string
contained in the QWT_LIB_BINARY variable. When compiling, the 'make' command
outputs the following line:
Project MESSAGE: QWT library name = qwt-qt4
When the temporary variable assignations are eliminated, like this:
QWT_LIB_BINARY=/usr/lib/libqwt-qt4.so
QWT_LIB_NAME = $$replace($$replace($$basename(QWT_LIB_BINARY), .so, ), lib, )
message(QWT library name = $$QWT_LIB_NAME)
The 'make' command outputs the message:
Project MESSAGE: QWT library name =
Indicating that the last code is not working correctly. Is it possible to
nest function calls in '.pro' files in some other way, so it can work?
Related
I am trying to use the selenium webdriver API directly from R using rJava. I am subject to a fairly restrictive IT environment, so I can't access a remote driver currently (hence why I'm not currently using the Rselenium package), and I don't have either Chrome or Firefox availaible--just phantomjs. I am able to get this working okay from the Scala REPL. I used sbt to get all the dependenices--build.sbt contains, for example:
retrieveManaged := true
libraryDependencies ++= Seq (
"org.seleniumhq.selenium" % "selenium-java" % "3.9.1",
"com.codeborne" % "phantomjsdriver" % "1.4.4"
)
(Note that I have phantomjs installed as /usr/local/bin/phantomjs, and it is
version 2.1.1).
I then copied all the jar files to a single-level folder via cp jars/*/*/*.jar alljars/ containing the following:
animal-sniffer-annotations-1.14.jar httpcore-4.4.6.jar selenium-api-3.9.1.jar
byte-buddy-1.7.9.jar j2objc-annotations-1.1.jar selenium-chrome-driver-3.9.1.jar
checker-compat-qual-2.0.0.jar jline-2.14.5.jar selenium-edge-driver-3.9.1.jar
commons-codec-1.10.jar jsr305-1.3.9.jar selenium-firefox-driver-3.9.1.jar
commons-exec-1.3.jar okhttp-3.9.1.jar selenium-ie-driver-3.9.1.jar
commons-logging-1.2.jar okio-1.13.0.jar selenium-java-3.9.1.jar
error_prone_annotations-2.1.3.jar phantomjsdriver-1.4.4.jar selenium-opera-driver-3.9.1.jar
gson-2.8.2.jar scala-compiler-2.12.4.jar selenium-remote-driver-3.9.1.jar
guava-23.6-jre.jar scala-library-2.12.4.jar selenium-safari-driver-3.9.1.jar
httpclient-4.5.3.jar scala-reflect-2.12.4.jar selenium-support-3.9.1.jar
I start Scala via scala -cp "alljars/*" and can the do following:
val drv = new org.openqa.selenium.phantomjs.PhantomJSDriver
drv.get("https://www.google.com")
val q = drv.findElementByName("q")
q.sendKeys("rJava selenium")
q.submit
drv.getTitle
I think the following is roughly the same thing in R using rJava:
library(rJava)
.jinit()
jars <- dir("alljars", pattern = "*.jar", full.names = TRUE)
.jaddClassPath(jars)
drv <- .jnew('org/openqa/selenium/phantomjs/PhantomJSDriver')
drv$get("https://www.google.com")
q <- drv$findElementByName("q")
q$sendKeys("rJava selenium")
q$submit()
drv$getTitle()
This fails at the point q$sendKeys("rJava selenium") with the following error:
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.lang.NoSuchMethodException: No suitable method for the given parameters
In RStudio, if I type q$ and press TAB, sendKeys is definitely in the list of available methods. I tried to be explicit about this, and tried:
keys <- .jnew("java/lang/String", "rJava selenium")
keys <- .jcast(keys, "java/lang/CharSequence", check = TRUE)
q <- .jcast(q, "org/openqa/selenium/WebElement", check = TRUE)
.jcall(q, "V", "sendKeys", keys)
which resulted in the following error:
Error in .jcall(q, "V", "sendKeys", keys) :
method sendKeys with signature (Ljava/lang/CharSequence;)V not found
q has class org/openqa/selenium/remote/RemoteWebElement in R, and org/openqa/selenium/WebElement in Scala; but in both cases the return is void and the required argument is CharSequence according to the javadocs. I tried a few variations of this--java.lang.String instead of CharSequence, RemoteWebElement instead of WebElement, etc., but no joy.
I doubt this is a problem with rJava, but I'm stumped nonetheless and need help!
Oh good grief. I didn't know about .jmethods. Running this:
> .jmethods(q, "sendKeys")
[1] "public void org.openqa.selenium.remote.RemoteWebElement.sendKeys(java.lang.CharSequence[])"
So, basically, my problem was that I was passing String instead of String[]. That is, instead of:
q$sendKeys("rJava selenium")
I can use:
q$sendKeys(.jarray("rJava selenium"))
The more you know...
I am trying to use qmake to include all files in a directory (this project is an external subversion project with hundreds of files). I am using qmake version 3.1.
What I tried was something like:
server_files = $$files($$PWD/server)
SOURCES += server_files(*.cpp, true)
The first line does not give any error but the second line gives:
:-1: warning: Failure to find: server_files(*.cpp,
:-1: warning: Failure to find: true)
Putting a $ sign in front of the variable as SOURCES += $server_files(*.cpp, true) gives the same error.
The following example function takes a variable name as its only argument, extracts a list of values from the variable with the eval() built-in function, and compiles a list of files:
defineReplace(headersAndSources) {
variable = $$1
names = $$eval($$variable)
headers =
sources =
for(name, names) {
header = $${name}.h
exists($$header) {
headers += $$header
}
source = $${name}.cpp
exists($$source) {
sources += $$source
}
}
return($$headers $$sources)
}
Variable Processing Functions
This is an R script for array quality metrics. The first step is going well but after the execution of the 2nd step an error occurs.
library(arrayQualityMetrics)
library(limma)
library(tcltk)
X <-tk_choose.files(caption = "Choose X")
maData<-read.maimages(X, source="agilent", other.columns = "g", green.only=TRUE)
eSet<-new("ExpressionSet", exprs = maData$other$g, annotation =maData$genes[,7])
arrayQualityMetrics(eSet, outdir="QC_C", force = TRUE, do.logtransform = TRUE)
The program is running now but it is showing this warning message:
The directory 'QC_C' has been created.
Warning messages:
1: In svgStyleAttributes(style) :
Removing non-SVG style attribute name(s): subscripts, group.number, group.value
2: In svgStyleAttributes(style) :
Removing non-SVG style attribute name(s): subscripts, group.number, group.value
Where am I getting wrong? Is this the errors in the file or the Rscript is wrong....
Give the full path of the folder under path as below:
scanFiles<-dir(path='/path/to/folder/',pattern = ".*.txt$")
I am attempting to use the Rcpp11 package in r from it's source over at:
devtools::install_github("Rcpp11/Rcpp11")
I read here: http://blog.r-enthusiasts.com/2014/05/27/disambiguating-rcpp11-and-rcpp/
that I can use include <Rcpp11> + using namespace Rcpp11 at the head of my .cpp file but I get this error upon sourcing:
egfile.cpp:1:10: fatal error: 'Rcpp11' file not found
#include <Rcpp11>
^
1 error generated.
where egfile.cpp:
#include <Rcpp11>
using namespace Rcpp11;
// Below is a simple example of exporting a C++ function to R. You can
// source this function into an R session using the Rcpp::sourceCpp
// function (or via the Source button on the editor toolbar)
// For more on using Rcpp click the Help button on the editor toolbar
// [[Rcpp::export]]
int timesTwo(int x) {
return x * 2;
}
Any help with this? or should I defer to the // [[Rcpp::plugins(cpp11)]] method ?
Update: using the attributes::sourceCpp()
devtools::install_github("Rcpp11/attributes")
then restart from a clean session:
library(Rcpp11)
attributes::sourceCpp("egfile.cpp") # in home directory.
I get:
In file included from file2c1e303c4ed6.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp11:4:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp.h:238:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:54:1: error: no member named 'Rf_pnorm' in the global namespace
RCPP_DPQ__2(norm,double mean = 0, double sd = 1, mean, sd )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:30:51: note: expanded from macro 'RCPP_DPQ__2'
#define RCPP_DPQ__2(__NAME__,PAR1,PAR2,VAL1,VAL2) RCPP_DPQ(__NAME__,RCPP_ECHO(RCPP_CONCAT(PAR1,PAR2)), RCPP_ECHO(RCPP_CONCAT(VAL1,VAL2)) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:14:31: note: expanded from macro 'RCPP_DPQ'
decltype(sapply( x, ::Rf_p##__NAME__, VAL, lower, log )) \
~~^
<scratch space>:208:1: note: expanded from here
Rf_pnorm
^
In file included from file2c1e303c4ed6.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp11:4:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp.h:238:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:54:1: error: no member named 'Rf_pnorm' in the global namespace
RCPP_DPQ__2(norm,double mean = 0, double sd = 1, mean, sd )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:30:51: note: expanded from macro 'RCPP_DPQ__2'
#define RCPP_DPQ__2(__NAME__,PAR1,PAR2,VAL1,VAL2) RCPP_DPQ(__NAME__,RCPP_ECHO(RCPP_CONCAT(PAR1,PAR2)), RCPP_ECHO(RCPP_CONCAT(VAL1,VAL2)) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:16:29: note: expanded from macro 'RCPP_DPQ'
return sapply( x, ::Rf_p##__NAME__, VAL, lower, log ) ; \
~~^
<scratch space>:208:1: note: expanded from here
Rf_pnorm
^
In file included from file2c1e303c4ed6.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp11:4:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp.h:238:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:54:1: error: no member named 'Rf_qnorm' in the global namespace
RCPP_DPQ__2(norm,double mean = 0, double sd = 1, mean, sd )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:30:51: note: expanded from macro 'RCPP_DPQ__2'
#define RCPP_DPQ__2(__NAME__,PAR1,PAR2,VAL1,VAL2) RCPP_DPQ(__NAME__,RCPP_ECHO(RCPP_CONCAT(PAR1,PAR2)), RCPP_ECHO(RCPP_CONCAT(VAL1,VAL2)) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:20:31: note: expanded from macro 'RCPP_DPQ'
decltype(sapply( x, ::Rf_q##__NAME__, VAL, lower, log )) \
~~^
<scratch space>:208:1: note: expanded from here
Rf_qnorm
^
In file included from file2c1e303c4ed6.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp11:4:
In file included from /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp.h:238:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:54:1: error: no member named 'Rf_qnorm' in the global namespace
RCPP_DPQ__2(norm,double mean = 0, double sd = 1, mean, sd )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:30:51: note: expanded from macro 'RCPP_DPQ__2'
#define RCPP_DPQ__2(__NAME__,PAR1,PAR2,VAL1,VAL2) RCPP_DPQ(__NAME__,RCPP_ECHO(RCPP_CONCAT(PAR1,PAR2)), RCPP_ECHO(RCPP_CONCAT(VAL1,VAL2)) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp11/include/Rcpp/stats/stats.h:22:29: note: expanded from macro 'RCPP_DPQ'
return sapply( x, ::Rf_q##__NAME__, VAL, lower, log ) ; \
~~^
<scratch space>:208:1: note: expanded from here
Rf_qnorm
^
4 errors generated.
make: *** [file2c1e303c4ed6.o] Error 1
Error in dyn.load(basename(dynlib)) :
unable to load shared object '/private/var/folders/77/9nq5hj5d37b1rhbzdt0z3twr0000gn/T/RtmpcjWOsg/file2c1e303c4ed6.so':
dlopen(/private/var/folders/77/9nq5hj5d37b1rhbzdt0z3twr0000gn/T/RtmpcjWOsg/file2c1e303c4ed6.so, 6): image not found
In addition: Warning message:
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB 'file2c1e303c4ed6.cpp'' had status 1
Presumably, you are trying to compile it from R Studio, which will use Rcpp::sourceCpp. You need the implementation of sourceCpp from the attributes package to generate the glue code for Rcpp11. attributes is available from github:
devtools::install_github("Rcpp11/attributes")
Then use this version to compile your file, i.e.
attributes::sourceCpp( "yourfile.cpp" )
Compiling an Rcpp11 file using Rstudio ui is something we have not yet dealt with, but something we identified as needed here
I recently rewrote a package to use the new(er) R reference class objects. I've exported the three classes using export() in the NAMESPACE file so as far as I'm aware that should work. However when I test build the package I get an error at lazy loading stage:
** preparing package for lazy loading
Error in file(con, "rb") : invalid 'description' argument
ERROR: lazy loading failed for package ‘PACKAGE_NAME_HERE’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/PACKAGE_NAME_HERE’
I'm not sure what the problem is here. I don't know if it's relevant but the reference classes do store data on files in the tmp directory by having some fields set as accessor functions - I don't know if that's what s being complained about here when it says (con, "rb") which I guess is some connection thing. Does anybody have any ideas or advice for making sure reference classes get exported properly? My namespace is currently simple -
export(Main)
export(Mainseq)
export(Maintriplet)
Which are the three reference classes I exported by using #export tags in roxygen2.
What is it I'm doing (or not doing) that is throwing the lazy load error?
(ASIDE - I have no compiled code - all R, although the reference class methods do call some internal functions that are not exported, but these are supposed to be internal so I don't think I need to export them.
Thanks,
Ben.
EDIT:
My description file is as follows:
Package: HybRIDS
Type: Package
Title: Quick detection and dating of Recombinant Regions in DNA sequence data.
Version: 1.0
Date: 2013-03-13
Author: Ben J. Ward
Maintainer: Ben J. Ward <b.ward#uea.ac.uk>
Description: A simple R package for the quick detection and dating of Recombinant Regions in DNA sequence data.
License: GPL-2
Depends: ggplot2,grid,gridExtra,png,ape
I can't see what is wrong with this - the Depends are correct.
EDIT:
I've eliminated the first error with the description but I'm still getting the con error.
I think it's because the Mainseq class (which is nested in class Main) has some fields:
FullSequenceFile = "character",
FullSequence = function( value ) {
if( missing( value ) ){
as.character( read.dna( file = FullSequenceFile, format = "fasta", as.matrix = TRUE ) )
} else {
write.dna( value, file = FullSequenceFile, format = "fasta" )
}
},
InformativeSequenceFile = "character",
InformativeSequence = function( value ) {
if( missing( value ) ){
as.character( read.dna( file = InformativeSequenceFile, format = "fasta", as.matrix = TRUE ) )
} else {
write.dna( value, file = InformativeSequenceFile, format = "fasta" )
}
}
The idea being upon initialisation, the two character fields are filled with a path to a temp file in tmpdir, and when the variables are called or edited the files containing the variable data are read or written to. However it seems the variables are being accessed before this path is available because up package build the following happens:
** preparing package for lazy loading
Warning in file(con, "rb") :
cannot open file '/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T//RtmpLB8ESC/FullSequenceaba52ac591f3': No such file or directory
Error in file(con, "rb") : cannot open the connection